In part 4, we'll use the same data as in part 3, but we'll make a stacked plot of it. This is a short post.

There is at least one other way of making a stacked plot in gnuplot, but it doesn't yield what I'd consider as being publication quality plots. It's also fairly restrictive in the type of data can be plotted. The method shown here is general and applicable to all types of data. You can e.g. use it for time-dependent NMR data...

And systemd makes troubleshooting this worse than necessary since the logs are binary. Seriously, the use of plain text files in linux for configuration and logs is one of the MAIN defining features of the OS.

Anyway, Arch is a fine OS. But I've been burned a few times too many now, and I am no longer young and have plenty of time and enthusiasm for this kind of stuff. I've just started installing debian instead...and for once I'm going straight for stable...

A contributing factor is that we use this computer as the family one, for watching tv, listening to music etc. And sitting down on a Sunday evening to relax and finding that the damned system won't even boot isn't a good way to end the weekend.

Anyway, if you are looking for a fix, all I can give you is my gut feeling -- downgrade. The old packages are in /var/cache/pacman/pkg

Why downloading the source and copying it? Because (imho) it's easier than fiddling with packages -- you can put the sources on a usb stick and copy it. But good luck, whatever method you try. I'm switching my second to last non-debian computer back to my main OS (i.e. debian). I've still got a Scientific Linux box, which I haven't booted for well over a month now...

26 July 2013

Update 18/8/2014: I've since done this on a unit with a BCM5357 chip rev 2 pkg 8 as well:

Update: the more I use it, the more I like it. I really like my old WRT54G, but I'm even happier about my fancy new E2500 since it's faster and all. Flashing them are equally easy. If you prefer some else to do it for you -- or if you want to seek independent confirmation that the router can be flashed -- look at http://flashrouters.com/ . The focus on that site seems to be dd-wrt (which is an alternative to Tomato), but they do list tomato routers too, e.g. http://www.flashrouters.com/routers/cisco-linksys-e2500-tomatousb-router

Original post:
Flashing a router is always a bit unsettling, so here's a detailed how-to.

Anyway, I managed to pick up a Linksys E2500-AU for $45 (Broadcom BCM5357 chip rev 1 pkg 8), which isn't too shabby. Some cursory searching showed that people had managed to put dd-wrt and tomato on it. While my experience with dd-wrt hasn't been that good, I've been running tomato on a linksys wrt45g for a around four years now, without any issues.

There's a number of derivatives of Tomato e.g. Tomato USB, and I'm a bit confused over what sets some of them apart. However, it seems like this Polish site is the right one for me. See here for the 'about' page.

What I'm presuming:
That you are running linux, and that you can afford to brick your router. There is always a risk associated with flashing firmware, and don't make any assumptions about the validity of the warranty...

With the router turned off, connect it via CAT5 cable to your computer. It should be attached to one of the LAN ports (in my case Ethernet 4) on the router. Ignore what the manual says about plugging into the WAN ('Internet') port.

Plug in power cable to the router.

On my computer I've disabled network manager (sudo rcconf, then uncheck network manager and either stop it or reboot) and my /etc/network/interfaces has this in it:

auto eth1
iface eth1 inet dhcp
ethernet-wol g

You probably won't have to worry about this. Just make sure that you don't have anything interfering with the 192.168.1.0/24 subnet.

Anyway, once you have been assigned an IP address, navigate to 192.168.1.1, and work your way through the annoying warnings:

leave the user name blank, and use admin as the password

Here's where it get's interesting. Select the .bin file you downloaded and hit ok.

Use admin for both username and password

I was then met with this, which at first scared me a little:

I unplugged the power from the router, and plugged it in again, and I could log in:

The first step is to erase the nvram, or you might end up with "Cannot proceed: two or more lan bridges have conflicting ip addresses or overlapping subnets" when configuring your network. To erase NVRAM go to Administration/Configuration/Restore Default Configuration - Erase all data in NVRAM memory(thorough).

You are now ready to start setting up your router.

Go to Administration/Admin access.

Set up an admin password, turn off telnet and change the colour scheme to Tomato. Optional but recommended: disable ssh access via password -- it's better if you add your public keys here.

Go to Basic/Network, and set an SSID and a password for your wireless. Set up your network details -- in my case I have static IP. I also want the subnet to be 192.168.2.0/24 and I use MAC spoofing, which you can set up under Advanced/MAC address.

23 July 2013

This post is primarily intended for two particular students. However, the problem it addresses is something that a lot of spectrometrists/scopists who want to take their data presentation to the next level have encountered.

In addition, for the specifics in the commands below I will presume that this data is based on a cone voltage sweep from 0 to 300 in 10 volt steps. I thus have a series of files named: 0.csv, 10.csv, 20.csv..190,300.csv.

You should be able to easily customize the approach to e.g. time or concentration dependent data.

Let's get started:0. Pre-reqs
Make sure you have gawk, sed, xargs, gnuplot, paste, python installed. On debian do

sudo apt-get install gawk sed xargs gnuplot paste python

1. Convert the csv files to dat files
Create the following script and call it csv2dat.sh

3. Pad the data with zeroes
Create a file called makelist.py, and put the following in it. Watch out for tab lengths etc. It's written for python 2.x, and probably won't work under python 3. It was also hacked together from an earlier script which didn't quite work the way I hoped it would.

6. Plot using gnuplot
See the following script for an example. Note that plotting in gnuplot using 'matrix' you don't get the benefit of proper axes labels. Instead we do a bit of on-the-fly maths to get the axes right. Specifically:

using (2999.3-(($1-1)/10)):(($2-1)*10):($3)

means that for the m/z axes ($1) we take the highest value (in our case 2999.3) and remove 0.1 m/z (our resolution) for each data point. This data is in each row. For the CV axes ($2), which goes down the columns in our matrix.rot.dat, we have thirty values. Each one corresponds to an increase in 10V starting at 0V, hence we multiply by 10. $3 is the intensity, which we don't need to fiddle with.

22 July 2013

My problem is that my computers are sitting behind a router (on a 192.168.2.0/24 subnet) and the computers that I want to access sit on the university network, to which the router is connected. The address range is, say, 131.172.x.x.

In other words, I (think I) want to use samba across two subnets.

I've opened up ports 13-139,445 to tcp and udp on both the router and in iptables on my desktop.

My problem:
1. I can't see the network shares of the other computers using
a) nautilus (Network/Windows Network)
b) nmblookup
c) sambascanner

2. I can't connect to network shares using their netbios names. For example, I'd like to connect to e.g. smb://avance400/data, but I have to use the IP address instead. For some curious reason not even that works using nautilus.

Workaround:
So here's not a solution, but a workaround.

I can connect to other computers from the command line as long as I know the IP address, and here's how

smbclient //131.172.123.30/data -U myuni/me

If you actually want to mount the share, which is password protected, and you do, then do

but supplying the password as part of the command line works, then you are missing cifs-utils, so install them.

Note that mount.cifs can handle credentials from a special file, e.g. like this , which you chmod to 600. My chief issue with that is that ~/.bash_history has exactly the same permissions (u+rw, go-rwx) and so I don't see how it's that's any safer than exposing everything by supplying your password as part of the mount command. Both should be avoided if possible.

On the other hand you could argue that since the password is transmitted over the network in cleartext you're inviting trouble either way...

NOTE: I've heard rumours about problems with Matt Monroe's calculator on Windows 7 Home, and on Windows 8. I've heard reports of it working on Windows 7 Professional. Given that wsearch also has issues, this may be linked to VB.

This post is, like this one, is written with two particular students in mind.

Our scenario:
So you've exported your data as e.g. data.csv, and you have assigned a signal in your spectrum to a species, and you'd now like to plot the predicted and observed isotopic envelopes in a way that will help you compare them.

The signal we have identified is at 211.90 m/z and we think it belongs to [Ga(CH3OH)2(OH)(NO3)]+.

In the spectrum window, go to Edit, Copy Data Points, and paste into e.g. a Gedit window. Save as 1.dat

2. Formatting the data.csv for gnuplot (can skip for spreadsheet programs):
In a single line we remove the first eight lines, replace all commans (,) with tabs, only keep the m/z and relative isotopic abundance columns (2 an 4) and save the output to data.dat

tail -n +8 data.csv |sed 's/\,/\t/g'|gawk '{print $2,$4}' > data.dat

3. Plotting:

A. Using gnuplot:
Create a file called 1.gplt which contains the gnuplot commands:

($1-0.05) means we're offsetting the calculated data by 0.05 m/z. ($2*0.092) means that we're scaling the calculated data intensity to match that of the observed. lc sets line colour and lw sets the width

If you want the output as png instead of eps, just change the first two lines to

set term png size 1000,667
set output '1.png'

Using pyisocalc

Using Matthew Monroe's calculator

B. Using QtiPlot
Qtiplot is in the debian repos and is 'origin'-like (as in Microcal Origin).

You'll need to rescaled your calculated data first, which is a major drawback:

cat 1.dat|gawk '{print $1-0.05,$2*0.095}'> 1_scaled.dat

Start QtiPlot and select Open. Make sure you select 'all files' as the file type. Open 1_scaled.dat.

Next, make sure that the spreadsheet is active, and go to File, Import, Import Ascii

Change the type of column 3

Select all columns and go to Plot, Line. Change the axes (double click on the axes and set the new ranges), set the top and right axes no to show, edit the titles etc.

Doing this on windows is a PITA compared to Linux, and I don't have the time to go through it. If you do have Origin, it should be straightforward to translate the instructions above into an MS Win-like environment.

Any scaling will have to be done in Excel or a similar spreadsheet program. Not difficult, but it'll add a few extra steps.

19 July 2013

popping up at the end of ./configure. I've added a fix for it based on http://forum.winehq.org/viewtopic.php?f=2&t=17713Original post:
Here's a generic way of building Wine 1.6 which is now stable. And yes, it's the instructions for 1.5.28-1.6-rcX recycled.

Getting started:
If you set up a e.g. chroot to build 1.5.28 you don't need to set up a new chroot to build 1.6. In that case, skip the set-up step below and instead re-enter your existing chroot like this:

Replace 'beryllium' with the name your host system (it's just to suppress error messages)Building Wine
While still in the chroot, continue (the i386 is ok; don't worry about it -- you don't actually need it):

17 July 2013

I need to transfer raw mass spec files off of the computer controlling our waters zmd, and it seems like I may be the only one in the department wishing to do so.

Since the computer is running Windows NT 4 and doesn't support USB drives out of the box, and I'm a bit worried about installing new software (e.g. old versions of filezilla via oldapps) on a computer on which a lot of people rely, I have two options:

* use SMB i.e. a windows share
or
* use ftp

I'm having all sorts of trouble getting my samba to work well at work -- my computers are sitting on a 192.168.2.0/24 LAN behind a router connected to the corporate network which has proper IP addresses (i.e. not using a reserved private network address space). I haven't managed to get my computer behind the router to 'see' the other computers and their shares at work beyond my router . I can, however, connect directly to the computers using e.g. smbclient -- they just won't show up in e.g. nautilus under windows network or using nmblookup. At any rate, connection directly to the target computer prompts me for a password and it seems that there are no open, accessible shares on that computer, only password protected ones.

Win NT has a DOS ftp client, so I finally decided to set up a quick and dirty ftp server on my workstation in my office so that I could transfer a couple of data files to figure out my other issue -- whether I have any piece of software that can actually open the masslynx .raw files. Turns out that neither wsearch32 nor openchrom can, so the exercise has been somewhat futile, although it has to be said that I'd like to be in charge of any raw data that leads to publications, and so I should be able to manage the storage of it myself.

Note: ftp is an inherently unsafe method since it doesn't use encryption. Use a separate user for this with no privileges, change the password of that user regularly, and close port 21 whenever you aren't using it in order to not advertise that you are running an ftp server. Use ssh/sftp if at all possible.

Essentially, OpenChrom now seems a lot easier and more natural to use.

The installation is the same as before (I've copied the old post below):1. Install Java v1.7 (need > 1.6)
You can either use openjdk 7 or (Oracle) Java. See here for a general guide to installing Oracle/Sun Java.

As for openjdk, you can easily install it:sudo apt-get install openjdk-7-jdk

(the openjdk-7-jre package is enough if you don't want the full developer's kit)

You can install plug-ins, e.g. to open Agilent files, by going to Plugins/OpenChrom Marketplace. Plugins will typically run for 30 days, but can be unlocked for perpetuity by adding a serial key, which is free. Add license keys by first registering on the openchrom website, going to http://www.openchrom.net/main/content/plugins.php, and clicking on the plugin you want a serial key for. You can then enter that key by going e.g. Window/Preferences/Converter in the OpenChrom software.

Everyone has their own idea of what a good piece of mass spec software should look like, and I suspect that OpenChrom caters to them all. Layouts are called Perspectives here. On the flip side, if you accidentally use a perspective that doesn't suit you, you may be incredibly frustrated until you figure out what's going on.

I like wsearch32, so my preferred view is to go to Window/Perspective Switcher -> Chromatogram MS (exact).

Opening spectra is much easier than before: now simply go to File/Open Chromatogram (MSD) and click on the file (or directory structure in the case of e.g. Agilent .D directories) and open:

Anyway, openchrom is getting better, is easier to use, and is still the only open source program that I know which can handle such an array of proprietary formats. Also, it can export data in both .csv and .xls formats, but you will need to install plugins for that, which is luckily very simple.

15 July 2013

I may have covered this at some point, but if so, I can't find the post.

Here's the situation:
You have a linux computer at work, which is behind a corporate firewall.
You have a router at home which runs an ssh server (e.g. running tomato).
You have a computer at home, which sits behind the router above.
You want to browse from home using the corporate network

In my case it's a little bit different -- I want to make a change to the router my office network (I have my own office) sits behind, and the easiest way to do that is by logging onto that router via http (it's a stock netgear router).

How to:
First, at work, connect to your home router using reverse ssh, so that all traffic on port 19999 on the router gets sent to port 22 on your work computer:

ssh -R 19999:localhost:22 root@myhomerouter

Later, at home, forward all traffic to port 8989 on your home computer to localhost:19999 on your router (which then gets sent to port 22 on your work computer):

ssh -L 8989:localhost:19999 root@192.168.2.1

We've assumed that the router sits on 192.168.2.1 from inside the LAN. Localhost here refers to your home computer, while localhost in the command before that refers to the router.

Then, in a different terminal, open a proxy through port 8989:

ssh -D 8888 me@localhost -p 8989

Finally, you can now edit your browser/network settings to use a SOCKS proxy on port 8888 like you would with any other proxy.

Here's yet another non-linux post. I'm currently getting ready for the start of the new semester and teaching, and so haven't had much time to work on improving my computer skills.

Anyway.

I've been advertising for an international PhD student for the past 9 months and have so far only had one great applicant and three acceptable applicants. That's out of ca 200 applicants in total.

So what does 'acceptable' mean? In this case my use actually agrees with the literal meaning -- students which will stand a chance of being accepted to the PhD program. It also means students which I could imagine working with.

The formal requirements will likely differ between different institutions, and between supervisors. In addition, some supervisors may be looking for different personalities in their prospective hires, than others.

I don't think that I'm being unnecessarily harsh in evaluating applicants, as I've had colleagues review my shortlists and who have thought I've even been a bit too optimistic in my evaluations.

At any rate, if you are looking for a PhD, be aware that there are a lot of applicants out there, and only a limited amount of money and places, so you will want to spend some time on your application.

So here are a few of my thoughts:
Before reading, keep in mind that I understand that applying for a PhD, especially if you are from the developing world and applying for a PhD position in the industrialised world, can be very tough, and sometimes depressing. You don't receive a reply to most of your applications, and when you do, they responses are normally negative.

* Try to familiarise yourself with the formal requirements, and address them in the first paragraph in your email to a prospective supervisor. In the case of my uni, there are two main requirements:
-- an undergraduate degree equivalent to a first class honour degree in Australia
-- a sufficiently good score at the IELTS

That's it. However, the hubris of many universities in Australia mean that the first requirement is a significant hurdle. Typically, good grades are just the beginning. In addition to that, the applicant needs to hold a masters degree (by research) and have a couple of papers in ISI rated journals. Obviously almost none of our own undergraduate students would meet that, but there you go.

So in your first paragraph, state what unis you did your degrees at, what your cumulative GPAs (or equivalent) were, how many papers you have published and what you overall band score AND section scores on the IELTS (or TOELF) are.

At this stage, that's much more important than your background, your hobbies, or anything else. If you can't meet the minimum requirements for entry to the PhD program, everything else doesn't matter.

* Read the advertisement, and follow any instructions
I ask applicants to submit all their documents as PDFs. Yet, I get plenty of applications with .doc, .docx, jpeg etc attached. You didn't read the instructions -- will you be more careful as a PhD student? Remember that you competing against plenty of applicants that did read the instructions.

Did I ask for your IELTS results? Didn't attach or mention them in your email/CV? Not a good sign. Also, it means that you're probably not a candidate.

* Address the supervisor and the supervisor's research
I get way, way too many emails that start with 'Dear Sir', or 'Dear Professor' or even worse: 'Dear Sir/Madam'. Put my name in there. It'll show me that you spent at least a few minutes on personalising your email. If you don't make that effort, why should I make the effort of reading your email and looking at your documents?

Also, please do mention the research of the supervisor you are applying to. It doesn't need to be anything insightful or special, but just write something like: 'I find your research into catalytic activation of molecules in ionic liquids very interesting.' or 'I read your article in Green Chemistry, 2013, 10, 2345 and found it very interesting. In particular, I liked how it showed how the selectivity of blah blah blah'.

The reason is not that you are showing off your great scientific skills (you've got an undergraduate degree -- we don't expect much), but that it shows you spent a bit of effort writing your email and personalising it. Also, flatter -- in moderation -- can occasionally help (don't go overboard, so be careful -- too much makes you seem insincere).

* Don't cold-call
This should go without saying. I've had one student email me in the morning, then call me in the afternoon. That kind of behaviour is probably correct if you are applying for certain jobs in the Real World (marketing?), but not for a PhD in chemistry. It's a sure-fire way of annoying people.

* Don't send a linked-in invite
I don't have time to scroll through your profile and try to compile a CV for you. Send me your CV in pdf format instead. Also, I don't know you, and have no incentive to add you to my 'network'.

* Be careful about 'hobbies' and 'interests'.
To me as a potential supervisor they really don't matter (again, this is my personal opinion). I know that the idea is to show that you are a well-rounded individual, but knowing that you like 'travel' or that you consider 'internet browsing' a skill will not be the edge that gets you into a PhD programme.

* 'It can't help you, only harm you'.
Keep this in mind. Unless it's a piece of information required in the advertisement, or that you are absolutely certain will help your application, consider leaving it out. You may include it to highlight a particular skill or trait, but remember that a CV can be interpreted ambiguously, and your intent may not be obvious. Instead, what you feel shows how independent and committed you are, can be seen as being unfocussed, a difficult person to work with, or simply attract attention away from more important aspects of your CV.

* Attending lectures, conferences
In their CVs, some applicants include lectures by famous people that they've attended, or conferences that they've gone to.

Here's the problem for me: most first year PhD students struggle with the notion that doing the work is no longer enough. Doing the experiments, or following your supervisor's instructions, is not enough. To get a PhD you need to make that extra effort and making things work. And if it doesn't work, you put in 150% effort -- the extra 50% being extra-curricular work on finding a related project that will work. Life as a PhD student can be easy if you are lucky, but most often is not -- life is incredibly good when you project is working, but on the flip-side it can be hard, depressing and demoralising when it isn't. You supervisor can alleviate some of that, but remember that your supervisor is only there to point you in a general direction -- the PhD is all about making the transition to becoming an INDEPENDENT research.

So be careful -- if you've presented posters or given talks at conferences or at other universities, you should definitely list them, but under a suitable heading -- NOT publications. They'll detract attention from the publications, and the publications is what will get you an offer of acceptance.

* Do not make things conditional
I had an applicant who was borderline (in terms of meeting the requirements), and in those cases occasionally the supervisor putting in extra effort into cajoling the university administration MAY be enough to get a student accepted (don't count on it). If your prospective supervisor asks you to re-take IELTS, don't write something along the lines of 'I will, but only if this is the last hurdle'.

I understand it's expensive, but remember: even if you meet all the requirements I cannot guarantee that you get accepted. And I can' wait months for each student to pass through the application system -- I need to hire someone now. So be proactive.

* Face-to-face (or skype/video) interview is a good sign
If your supervisor asks for a skype interview, this is a great sign. And likely this isn't really done in order to gauge your scientific skills, but just to get a feel for your personality. Also, it's a way of making sure that your English levels are good enough that you can communicate with your supervisor. Finally, if you are borderline in terms of IELTS/TOELF, your supervisor may be able to argue that you English is good enough based on that interview. So take the opportunity.

And send an email a few hours after the interview thanking for the opportunity. 1-2 lines is enough. It will show that you're a decent human being.

* Be prompt in replying to emails
It doesn't matter what stage of the application you are at -- until the paperwork has been signed you are still on probation. If you take several days to reply to any of my emails, then you are likely to be dropped. The reason is simple: if you take a week to get things done when you are a PhD student, then you will be a disaster for me. A disaster that I'll have to live with for the next 3-4 years, and whom will be using up my research grant, and potentially ruining my career.

I understand that the reason for you being slow may be different -- maybe you are just nervous, maybe you have nothing to say, maybe you feel you are intruding. Still, be prompt.

So:
if you can show that you can read and follow instructions, and if you can make my life easy by addressing the selection criteria in a clear way, and if you seem like a person I might enjoy working with for the next 3-4 years, then you stand a fair chance of getting an offer.

If I think you'll need constant supervision, is sloppy and won't follow instructions, or that our personalities will clash, I'll probably avoid you no matter how good your grades are.

10 July 2013

Many, many years ago I learned basic programming using BASIC (the version that came with PC DOS 5, I think). I even wrote the odd game, but it was all pretty awful. A few years later I learned Turbo Pascal, which was a fantastic experience compared to Basic. It felt all sciency and grown up, and it was my first experience with a real IDE. I even ended up buying a TP book, and became somewhat proficient. This must've been when I was around 18-19.I then stopped programming completely.

At around 30 years of age I decided it was time to get serious about programming again -- I was doing mass spectrometry and needed a simple program that could generate a series of solutions to the identity of a mass/charge ratio given a range of elements. I probably had a quick look at C and C++, but ended up getting a Python book and have been happy Python programmer ever since.

The problem is that I've never been a /good/ python programmer -- and in all these years I've never fully understood the use for (or, in all fairness, use OF) OOP. And at the moment it seems to be holding me back -- all the examples that I find of the use the threading module as well as writing GUIs (using e.g. wxPython) involve using classes. And I just don't understand them well enough to sort out what I need done.

Currently:
* the code is a mess (see above)
* it works fine for doing monotonic and dynamic end point titrations (MET and DET)
* it saves data to a file, but does so silently (i.e. when you run you won't get any feedback that things are working properly...)
* it uses the thread (not threading) module
* I've managed to pass parameters back and forth between the thread and the main loop using Queue

There are probably much better solutions. One day I hope to be able to stick a GUI on top of it, but the more I look at it I get the impression that one writes the GUI first, then the engine...not that I'd know.

Anyway. That's what I've been up to. Anyone with a bit of programming experience, whom is in possession of an old-school Titrino (i.e. using RS 232) and wants to save $1.5k in software licenses may be interested in taking the sources and turning them into something useful.

03 July 2013

I'm not going to leave much in the way of a comment, but this doesn't seem to have been publicised enough. Searching the web quickly didn't bring this up at all, and it's a shame since it's important, in particular if you are an Iranian national thinking about doing a PhD in Australia.

About a week ago the faculty in the chemistry department at my university were informed that heavy restrictions in terms of access to instrumentation has been put in place for students from North Korea, Syria and Iran via Federal legislation.

While I don't think there are any students from North Korea or Syria around, there are several Iranian students at different stages of their PhD. In fact, I would say around 50% of our applicants are from India, 25% are from Pakistan and 20 % are from Iran (in terms of accepted students the ratio is very different)

In practical terms, this means that Iranian students in the department are not allowed to use:
FT-IR
UV-Vis
NMR
Mass spectrometers
Raman
dosimeters
OES/AAS
etc.

All of which are standard instruments which most chemists would find necessary to do research. In addition, they can hardly be considered as being cutting edge, trade secrets or anything like that -- commercial NMR instruments have been around since the 1950s, infrared an UV/Visible spectroscopy go much further back. Mass spectrometry is a standard tool which, although many of the current designs only go back to the 1980s (e.g. ESI), is so conceptually simple and innocuous, that (to me) restrictions on it doesn't make sense. And so on.

In addition, supervisors of Iranian students have been asked to draw up a risk management plan to prevent student access to the above instruments, which is a particular problem given that they are used in teaching as well, and are available on a walk-in basis to undergraduate students doing projects in research labs.

Currently, any supervisor who has an Iranian student needing to use any of the instruments above will need to assign another student to do these measurements for the Iranian national.

While this doesn't formally preclude Iranians from coming to Australia to do a PhD, we have been advised that we should reject any applicants at this point. This may change once the university has figured out exactly where they must draw the line in terms of restricting access to Iranians to different facilities, but for now it's a blanket ban.

My personal opinion is that while you'd be led by the media to think of anyone from North Korea, Syria and Iran as potential spies, these are real people too. Many Iranians would either be completely disinterested in politics, or actively antipathetic to their regime. And the best thing about democracies -- we shouldn't have any issues with them supporting their government either. So I don't really agree with this as a security measure to prevent nuclear proliferation, which must surely be the stated goal.

And if the idea is to put in place sanctions to promote regime change, then why limit the type of instrumentation that students can access? Or are we trying to punish the children of the leadership in Iran? Then why not limit the sanctions to those specifically? Top students tend to come from all socioeconomic classes.

The timing is also very odd, given the recent election of a moderate.

And why Iran and not Belarus, China, Zimbabwe etc.?

Again, I don't like putting opinion pieces on this blog (other than as minor parts/rants of posts with actual content) but I think this should be publicized more.

Now what happens when I log in to gnome via gdm3 I get an empty desktop with no menus, no hot-spots or anything else indicating that things worked out. Alt+F2 doesn't work either, and conky doesn't start.

The only thing that does work is
* my keyboard shortcuts (I've mapped ctrl+shift+Down arrow to chromium)
* guake (which starts with gnome)

The jobs were run using all cores available on that node.
gnu= gfortran + acml 5.3.1 for the Phenom and FX8150, and openblas for the i5-2400 and the Athlon 3800+..ifort= ifort + mkl for all architectures.

In the last case I also compiled using gfortran but with mkl and got 1550s.

It's a fairly small sample set, but it does seem that there's a little bit of an advantage with mkl+ifort over gfortran+acml on the newest AMD core. One would need much more data though.

A clear downside of using mkl and ifort is the fact that they are not freely available though -- i.e. you can register and download them for free for non-commercial use, but there's no guarantee that your colleague, next-door-neighbour or distant-cousin will be able to use it.

Step no: 1 of 7 | Welcome
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Welcome to the Intel(R) Parallel Studio XE 2013 Update 3 for Linux* installation
program.
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You will complete the steps below during this installation:
Step 1 : Welcome
Step 2 : License
Step 3 : Activation
Step 4 : Intel(R) Software Improvement Program
Step 5 : Options
Step 6 : Installation
Step 7 : Complete
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Press "Enter" key to continue or "q" to quit:
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Checking the prerequisites. It can take several minutes. Please wait...
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Step no: 1 of 7 | Options > Missing Optional Pre-requisite(s)
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There are one or more optional unresolved issues. It is highly recommended to
resolve them all before you continue the installation. You can fix them without
exiting from the installation and re-check. Or you can quit from the
installation, fix them and run the installation again.
--------------------------------------------------------------------------------
Missing optional pre-requisites
-- Intel(R) VTune(TM) Amplifier XE 2013 Update 5: unsupported OS
-- Intel(R) Inspector XE 2013 Update 5: unsupported OS
-- Intel(R) Advisor XE 2013 Update 2: unsupported OS
-- Intel(R) Composer XE 2013 Update 3 for Linux*: unsupported OS
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1. Skip missing optional pre-requisites [default]
2. Show the detailed info about issue(s)
3. Re-check the pre-requisites
h. Help
b. Back to the previous menu
q. Quit
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Please type a selection or press "Enter" to accept default choice [1]:
Step no: 2 of 7 | License
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As noted in the Intel(R) Software Development Product End User License
Agreement, the Intel(R) Software Development Product you install will send Intel
[..]
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Do you agree to be bound by the terms and conditions of this license agreement?
Type "accept" to continue or "decline" to back to the previous menu: accept
Step no: 3 of 7 | Activation
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If you have purchased this product and have the serial number and a connection
to the internet you can choose to activate the product at this time. Activation
is a secure and anonymous one-time process that verifies your software licensing
rights to use the product. Alternatively, you can choose to evaluate the
product or defer activation by choosing the evaluate option. Evaluation software
will time out in about one month. Also you can use license file, license
manager, or remote activation if the system you are installing on does not
have internet access activation options.
--------------------------------------------------------------------------------
1. I want to activate my product using a serial number [default]
2. I want to evaluate my product or activate later
3. I want to activate either remotely, or by using a license file, or by using a
license manager
h. Help
b. Back to the previous menu
q. Quit
--------------------------------------------------------------------------------
Please type a selection or press "Enter" to accept default choice [1]:
Note: Press "Enter" key to back to the previous menu.
Please type your serial number (the format is XXXX-XXXXXXXX):
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Activation completed successfully.
--------------------------------------------------------------------------------
Press "Enter" key to continue:
Step no: 4 of 7 | Intel(R) Software Improvement Program
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Help improve your experience with Intel(R) software
Participate in the design of future Intel software. Select 'Yes' to give us
permission to learn about how you use your Intel software and we will do the
rest.
- No Personal contact information is collected
- There are no surveys or additional follow-up emails by opting in
- You can stop participating at any time
Learn more about Intel(R) Software Improvement Program
http://software.intel.com/en-us/articles/software-improvement-program
With your permission, Intel may automatically receive anonymous information
about how you use your current and future Intel software.
--------------------------------------------------------------------------------
1. Yes, I am willing to participate and improve Intel software. (Recommended)
2. No, I don't want to participate in the Intel(R) Software Improvement Program
at this time.
b. Back to the previous menu
q. Quit
--------------------------------------------------------------------------------
Please type a selection:
Step no: 5 of 7 | Options
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You are now ready to begin installation. You can use all default installation
settings by simply choosing the "Start installation Now" option or you can
customize these settings by selecting any of the change options given below
first. You can view a summary of the settings by selecting
"Show pre-install summary".
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1. Start installation Now
2. Change install directory [ /opt/intel ]
3. Change components to install [ All ]
4. Change advanced options
5. Show pre-install summary
h. Help
b. Back to the previous menu
q. Quit
--------------------------------------------------------------------------------
Please type a selection or press "Enter" to accept default choice [1]:
--------------------------------------------------------------------------------
Checking the prerequisites. It can take several minutes. Please wait...
--------------------------------------------------------------------------------
Step no: 5 of 7 | Options > Missing Optional Pre-requisite(s)
--------------------------------------------------------------------------------
There are one or more optional unresolved issues. It is highly recommended to
resolve them all before you continue the installation. You can fix them without
exiting from the installation and re-check. Or you can quit from the
installation, fix them and run the installation again.
--------------------------------------------------------------------------------
Missing optional pre-requisites
-- Intel(R) VTune(TM) Amplifier XE 2013 Update 5: The system does not have an
Intel Architecture processor
--------------------------------------------------------------------------------
1. Skip missing optional pre-requisites [default]
2. Show the detailed info about issue(s)
3. Re-check the pre-requisites
h. Help
b. Back to the previous menu
q. Quit
--------------------------------------------------------------------------------
Please type a selection or press "Enter" to accept default choice [1]:
Step no: 7 of 7 | Complete
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Thank you for installing and using the
Intel(R) Parallel Studio XE 2013 Update 3 for Linux*
Reminder: Intel(R) VTune(TM) Amplifier XE users must be members of the "vtune"
permissions group in order to use Event-based Sampling.
To register your product purchase, visit
https://registrationcenter.intel.com/RegCenter/registerexpress.aspx?clientsn=N43
3-4XGWTJLB
To get started using Intel(R) VTune(TM) Amplifier XE 2013 Update 5:
- To set your environment variables: source
/opt/intel/vtune_amplifier_xe_2013/amplxe-vars.sh
- To start the graphical user interface: amplxe-gui
- To use the command-line interface: amplxe-cl
- For more getting started resources: /opt/intel/vtune_amplifier_xe_2013/
documentation/en/welcomepage/get_started.html.
To get started using Intel(R) Inspector XE 2013 Update 5:
- To set your environment variables: source
/opt/intel/inspector_xe_2013/inspxe-vars.sh
- To start the graphical user interface: inspxe-gui
- To use the command-line interface: inspxe-cl
- For more getting started resources: /opt/intel/inspector_xe_2013/
documentation/en/welcomepage/get_started.html.
To get started using Intel(R) Advisor XE 2013 Update 2:
- To set your environment variables: source
/opt/intel/advisor_xe_2013/advixe-vars.sh
- To start the graphical user interface: advixe-gui
- To use the command-line interface: advixe-cl
- For more getting started resources: /opt/intel/advisor_xe_2013/
documentation/en/welcomepage/get_started.html.
To get started using Intel(R) Composer XE 2013 Update 3 for Linux*:
- Set the environment variables for a terminal window using one of the
following (replace "intel64" with "ia32" if you are using a 32-bit
platform).
For csh/tcsh:
$ source /opt/intel/bin/compilervars.csh intel64
For bash:
$ source /opt/intel/bin/compilervars.sh intel64
To invoke the installed compilers:
For C++: icpc
For C: icc
For Fortran: ifort
To get help, append the -help option or precede with the man command.
- For more getting started resources:
/opt/intel/composer_xe_2013/Documentation/en_US/get_started_lc.htm.
/opt/intel/composer_xe_2013/Documentation/en_US/get_started_lf.htm.
To view movies and additional training, visit
http://www.intel.com/software/products.
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q. Quit [default]
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Please type a selection or press "Enter" to accept default choice [q]:

The Files and Setup:
The compiler binaries are now found in /opt/intel/composer_xe_2013.3.163/bin/intel64/
. Of particular interest are ifort, icc and icpc (fortran, c and c++).

In addition, you'll need the lib and include files, which are found in /opt/intel/composer_xe_2013.3.163/compiler/lib/intel64/ and /opt/intel/composer_xe_2013.3.163/compiler/include/intel64.

You can either simply add the libs using LD_LIBRARY_PATH, but a perhaps easier and better method is to create a file: /etc/ld.so.conf.d/intel.conf